[gmx-users] g_rmsf Analysis.
Hello, I am using g_rmsf for analysis of a protein simulation. I want to calculate the fluctuations with respect to a reference structure (using -od option). But I am encountering a problem. Please correct me if I am wrong at some place. The following two methods are giving me different results. I have defined the residues forming helices as a separate group in the index file (to exclude loops). 1. g_rmsf -f abc.xtc -s abc.tpr -od rmsdev.xvg -n index -- I choose Protein_CA from the index file (full protein). 2. g_rmsf -f abc.xtc -s abc.tpr -od rmsdev.xvg -n index -- I choose helix_residues_CA from the index file (excluding loops). For the same helical regions of the protein I am getting different results from these two methods. The first one shows high fluctuations as compared to the second. My guess is that it can be due to different fitting by the choice of different atoms. But I suspect that the difference between the two is quite big than to be caused by different fitting. I also repeated the same analysis by dividing the trajectory into two parts and comparing the fluctuations with each other and the for the complete trajectory. The output in this case from the first method was consistent. Same regions were showing similar fluctuations. But for the second method the chunked parts of the trajectory displayed very small movement in certain regions where the complete trajectory analysis exhibited high fluctuations. How can this be inconsistent for the same fitting. Let me know if I am doing a mistake. Thanks. Vivek Modi Graduate Student, IITK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_rmsf Analysis.
On 4/25/13 10:12 AM, Vivek Modi wrote: Hello, I am using g_rmsf for analysis of a protein simulation. I want to calculate the fluctuations with respect to a reference structure (using -od option). But I am encountering a problem. Please correct me if I am wrong at some place. The following two methods are giving me different results. I have defined the residues forming helices as a separate group in the index file (to exclude loops). 1. g_rmsf -f abc.xtc -s abc.tpr -od rmsdev.xvg -n index -- I choose Protein_CA from the index file (full protein). 2. g_rmsf -f abc.xtc -s abc.tpr -od rmsdev.xvg -n index -- I choose helix_residues_CA from the index file (excluding loops). For the same helical regions of the protein I am getting different results from these two methods. The first one shows high fluctuations as compared to the second. My guess is that it can be due to different fitting by the choice of different atoms. But I suspect that the difference between the two is quite big than to be caused by different fitting. I would counter that differences in fitting can quite easily explain the difference you are seeing. Without the actual numbers, it's hard to say exactly. I also repeated the same analysis by dividing the trajectory into two parts and comparing the fluctuations with each other and the for the complete trajectory. The output in this case from the first method was consistent. Same regions were showing similar fluctuations. But for the second method the chunked parts of the trajectory displayed very small movement in certain regions where the complete trajectory analysis exhibited high fluctuations. How can this be inconsistent for the same fitting. Simply splitting the trajectory in half is not necessarily informative, especially if the structure is sampling different states, is not equilibrated in the beginning, etc. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_rmsf
Hi Efrat, 2011/5/3 Efrat Noy exlr...@mail.biu.ac.il: Hi, I have 2 questions regarding root mean square fluctuation calculations: 1. what exactly is the difference between the values in the rmsf.xvg file and the values in the rmsdev.xvg file (obtained with the -od option)? Are the rmsf.xvg values are standard deviations of atom positions along the trajectory with respect to an average structure of the trajectory? And rmsdev.xvg values are the same but in respect to a reference structure defined by the tpr file? The help is pretty clear on the first part: -od gives the RMSD w.r.t. the reference. You're right on the nature of the RMSF. 2. Is it possible to fit the trajectory structures, prior to rmsf calculations, on only part of the protein? Yes. You can preprocess the trajectory with trjconv and use the -nofit option to g_rmsf. Cheers, Tsjerk Thanks, Efrat -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_rmsf
Hi, I am just curious that in the MD community whether there is consensus on how to compare calculated rmsfs and expermental b-factors in x-ray. Should we use average value per residue or one particular atom in a residue for comparsion. Secondly, in NMR, people minimize a number of final calculated structures with energy minimization. Do people do the same thing when they average their structures within a certain time period with g_rmsf or g-covar. Thanks for your insight. Simon Sham -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_rmsf
Dear all, I want to calculate the C-alfa fluctuation of a protein during a trajectory with g_rmsf but I have just one question about the otput: which is the difference using -o output and -od output? So what is the difference between fluctuation and deviation? Thanks a lot in advance. Valerio This message was sent using IMP, the Internet Messaging Program. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_rmsf
vferra...@units.it wrote: Dear all, I want to calculate the C-alfa fluctuation of a protein during a trajectory with g_rmsf but I have just one question about the otput: which is the difference using -o output and -od output? So what is the difference between fluctuation and deviation? http://en.wikipedia.org/wiki/Root_mean_square_fluctuation http://en.wikipedia.org/wiki/Root_mean_square_deviation Other information in MD textbooks may be useful. -Justin Thanks a lot in advance. Valerio This message was sent using IMP, the Internet Messaging Program. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_rmsf
Thanks a lot. Valerio Justin A. Lemkul jalem...@vt.edu ha scritto: vferra...@units.it wrote: Dear all, I want to calculate the C-alfa fluctuation of a protein during a trajectory with g_rmsf but I have just one question about the otput: which is the difference using -o output and -od output? So what is the difference between fluctuation and deviation? http://en.wikipedia.org/wiki/Root_mean_square_fluctuation http://en.wikipedia.org/wiki/Root_mean_square_deviation Other information in MD textbooks may be useful. -Justin Thanks a lot in advance. Valerio This message was sent using IMP, the Internet Messaging Program. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists This message was sent using IMP, the Internet Messaging Program. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_rmsf reference structure?
Hi, The reference is used for fitting. The RMSF is calculated with respect to the average (fitted) structure, unless you explicitly specify that deviations from the reference should be used. Cheers, Tsjerk On Wed, Feb 16, 2011 at 7:08 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 16/02/2011 3:44 PM, kulleperuma.kulleper...@utoronto.ca wrote: Dear all, I use g_rmsf of Gromacs VERSION 4.0.5 to calculate the RMSF of the C-atoms with reference to the average structure between 5-10 ns of a total of 10 ns simulation as below; g_rmsf ?f md.xtc ?s md.tpr ?b 5000 ?e 1 ?o rmsf.xvg My understanding of the RMSF is as follows; RMSF = sqrt( 1/T ?[(xi(t)-Xi)]^2) where T is the time over which one wants to average, and Xi is the reference position of particle i, which is the time-averaged position of the same particle i. What I am confused is whether g_rmsf takes the reference structure from the structure file (-s), which in my case, the md.tpr and NOT the time averaged position over the specified time? It does take the reference structure from -s. Whether you actually want the RMSF from the non-physical time-averaged structure is up to you. IIRC you might be able to get such an average from g_cluster. Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_rmsf reference structure?
Dear all, I use g_rmsf of Gromacs VERSION 4.0.5 to calculate the RMSF of the C-atoms with reference to the average structure between 5-10 ns of a total of 10 ns simulation as below; g_rmsf ?f md.xtc ?s md.tpr ?b 5000 ?e 1 ?o rmsf.xvg My understanding of the RMSF is as follows; RMSF = sqrt( 1/T ?[(xi(t)-Xi)]^2) where T is the time over which one wants to average, and Xi is the reference position of particle i, which is the time-averaged position of the same particle i. What I am confused is whether g_rmsf takes the reference structure from the structure file (-s), which in my case, the md.tpr and NOT the time averaged position over the specified time? Thanking in advance for clarification. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_rmsf reference structure?
On 16/02/2011 3:44 PM, kulleperuma.kulleper...@utoronto.ca wrote: Dear all, I use g_rmsf of Gromacs VERSION 4.0.5 to calculate the RMSF of the C-atoms with reference to the average structure between 5-10 ns of a total of 10 ns simulation as below; g_rmsf ?f md.xtc ?s md.tpr ?b 5000 ?e 1 ?o rmsf.xvg My understanding of the RMSF is as follows; RMSF = sqrt( 1/T ?[(xi(t)-Xi)]^2) where T is the time over which one wants to average, and Xi is the reference position of particle i, which is the time-averaged position of the same particle i. What I am confused is whether g_rmsf takes the reference structure from the structure file (-s), which in my case, the md.tpr and NOT the time averaged position over the specified time? It does take the reference structure from -s. Whether you actually want the RMSF from the non-physical time-averaged structure is up to you. IIRC you might be able to get such an average from g_cluster. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_rmsf = average over # of time frames ???
If the reference structure from which the fluctuations are measured is taken
from the -s file (check the documentation or code), then a non-equilibrium
trajectory could well have this property w.r.t. a crystal structure.
Mark
- Original Message -
From: Chih-Ying Lin chihying2...@gmail.com
Date: Tuesday, October 26, 2010 15:55
Subject: [gmx-users] g_rmsf = average over # of time frames ???
To: gmx-users@gromacs.org
Hi
From source code = gmx_rmsf.c g_rmsf computes the root mean square
fluctuation (RMSF, i.e. standard ,
deviation) of atomic positions ,
if (devfn) {
/* Calculate RMS Deviation */
for(i=0;(iisize);i++) {
aid = index[i];
for(d=0;(dDIM);d++) {
rmsd_x[i][d] += sqr(x[aid][d]-xref[aid][d]);
}
}
}
count += 1.0;
rmsf[i] = (rmsd_x[i][XX]+rmsd_x[i][YY]+rmsd_x[i][ZZ])/count;
Therefore, g_rmsf is the average of structure deviation over the time frames.
However, I issued the commands ( C-alpha is selected )
g_rmsf -f abc.xtc -b 0 -e 100 -s abc-crystal.tpr -o RMSF-abc-0th-100th.xvg
g_rmsf -f abc.xtc -b 100 -e 200 -s abc-crystal.tpr -o
RMSF-abc-100th-200th.xvg
g_rmsf -f abc.xtc -b 200 -e 300 -s abc-crystal.tpr -o RMSF-abc-200th-300th.xvg
g_rmsf -f abc.xtc -b 300 -e 400 -s abc-crystal.tpr -o
RMSF-abc-300th-400th.xvg
g_rmsf -f abc.xtc -b 400 -e 500 -s abc-crystal.tpr -o
RMSF-abc-400th-500th.xvg
g_rmsf -f abc.xtc -b 500 -e 600 -s abc-crystal.tpr -o RMSF-abc-500th-600th.xvg
g_rmsf -f abc.xtc -b 600 -e 700 -s abc-crystal.tpr -o
RMSF-abc-600th-700th.xvg
g_rmsf -f abc.xtc -b 700 -e 800 -s abc-crystal.tpr -o
RMSF-abc-700th-800th.xvg
g_rmsf -f abc.xtc -b 800 -e 900 -s abc-crystal.tpr -o RMSF-abc-800th-900th.xvg
g_rmsf -f abc.xtc -b 900 -e 1000 -s abc-crystal.tpr -o
RMSF-abc-900th-1000th.xvg
Also, ( C-alpha is selected )
g_rmsf -f abc.xtc -b 0 -e 1000 -s abc-crystal.tpr -o RMSF-abc-0th-1000th.xvg
Then I ploted,
RMSF-abc-0th-100th.xvg
RMSF-abc-100th-200th.xvg
RMSF-abc-200th-300th.xvg
RMSF-abc-300th-400th.xvg
RMSF-abc-400th-500th.xvg
RMSF-abc-500th-600th.xvg
RMSF-abc-600th-700th.xvg
RMSF-abc-700th-800th.xvg
RMSF-abc-800th-900th.xvg
RMSF-abc-900th-1000th.xvg
Also, I ploted
RMSF-abc-0th-1000th.xvg
The PLOT RMSF-abc-0th-1000th.xvg has all RMSF-Values much higher than those
from RMSF-abc-0th-100th.xvg / RMSF-abc-100th-200th.xvg /
RMSF-abc-200th-300th.xvg / .. / RMSF-abc-900th-1000th.xvg...
It does not make sense... I supposed.
Did I misunderstand something ?
THank you
Lin
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_rmsf = average over # of time frames ???
Hi,
Lin, please think your questions over thoroughly in stead of flushing
every thought right to the mailing list. It also helps to stick to a
certain subject (reply) to make sure everything ends up in the same
thread. Maybe it's not a bad idea to read over
http://www.catb.org/esr/faqs/smart-questions.html (again).
Anyway, this question's quite valid :), and Marks answer is a bit
off... The reference structure for computing the RMSF is only used for
fitting; you'd also have seen this behaviour if you'd taken an average
structure from an equilibrium simulation. The fluctuations are around
the mean structure. The larger fluctuations in the first part of the
simulation are caused by the relaxation from the starting structure.
oversimplificationIf you think of the starting structure and the
'equilibrium structure' as position A and B, then the first part shows
you the mean squared deviation of the path from A to B around (A+B)/2,
whereas the next parts give you the mean squared deviation around
B/oversimplification. Note that this gives you a means to assess
whether you've reached equilibrium, albeit not a sufficient measure.
Hope it helps,
Tsjerk
On Tue, Oct 26, 2010 at 8:24 AM, Mark Abraham mark.abra...@anu.edu.au wrote:
If the reference structure from which the fluctuations are measured is taken
from the -s file (check the documentation or code), then a non-equilibrium
trajectory could well have this property w.r.t. a crystal structure.
Mark
- Original Message -
From: Chih-Ying Lin chihying2...@gmail.com
Date: Tuesday, October 26, 2010 15:55
Subject: [gmx-users] g_rmsf = average over # of time frames ???
To: gmx-users@gromacs.org
Hi
From source code = gmx_rmsf.c
g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard ,
deviation) of atomic positions ,
if (devfn) {
/* Calculate RMS Deviation */
for(i=0;(iisize);i++) {
aid = index[i];
for(d=0;(dDIM);d++) {
rmsd_x[i][d] += sqr(x[aid][d]-xref[aid][d]);
}
}
}
count += 1.0;
rmsf[i] = (rmsd_x[i][XX]+rmsd_x[i][YY]+rmsd_x[i][ZZ])/count;
Therefore, g_rmsf is the average of structure deviation over the time
frames.
However, I issued the commands ( C-alpha is selected )
g_rmsf -f abc.xtc -b 0 -e 100 -s abc-crystal.tpr -o RMSF-abc-0th-100th.xvg
g_rmsf -f abc.xtc -b 100 -e 200 -s abc-crystal.tpr -o
RMSF-abc-100th-200th.xvg
g_rmsf -f abc.xtc -b 200 -e 300 -s abc-crystal.tpr -o
RMSF-abc-200th-300th.xvg
g_rmsf -f abc.xtc -b 300 -e 400 -s abc-crystal.tpr -o
RMSF-abc-300th-400th.xvg
g_rmsf -f abc.xtc -b 400 -e 500 -s abc-crystal.tpr -o
RMSF-abc-400th-500th.xvg
g_rmsf -f abc.xtc -b 500 -e 600 -s abc-crystal.tpr -o
RMSF-abc-500th-600th.xvg
g_rmsf -f abc.xtc -b 600 -e 700 -s abc-crystal.tpr -o
RMSF-abc-600th-700th.xvg
g_rmsf -f abc.xtc -b 700 -e 800 -s abc-crystal.tpr -o
RMSF-abc-700th-800th.xvg
g_rmsf -f abc.xtc -b 800 -e 900 -s abc-crystal.tpr -o
RMSF-abc-800th-900th.xvg
g_rmsf -f abc.xtc -b 900 -e 1000 -s abc-crystal.tpr -o
RMSF-abc-900th-1000th.xvg
Also, ( C-alpha is selected )
g_rmsf -f abc.xtc -b 0 -e 1000 -s abc-crystal.tpr -o
RMSF-abc-0th-1000th.xvg
Then I ploted,
RMSF-abc-0th-100th.xvg
RMSF-abc-100th-200th.xvg
RMSF-abc-200th-300th.xvg
RMSF-abc-300th-400th.xvg
RMSF-abc-400th-500th.xvg
RMSF-abc-500th-600th.xvg
RMSF-abc-600th-700th.xvg
RMSF-abc-700th-800th.xvg
RMSF-abc-800th-900th.xvg
RMSF-abc-900th-1000th.xvg
Also, I ploted
RMSF-abc-0th-1000th.xvg
The PLOT RMSF-abc-0th-1000th.xvg has all RMSF-Values much higher than
those from RMSF-abc-0th-100th.xvg / RMSF-abc-100th-200th.xvg
/ RMSF-abc-200th-300th.xvg / .. / RMSF-abc-900th-1000th.xvg...
It does not make sense... I supposed.
Did I misunderstand something ?
THank you
Lin
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Re: [gmx-users] g_rmsf -res = average over time for each residue?
Hi Lin, How many residues do you have and how many points do you get? (Only answer for yourself). We're no substitute for your brain, you know... Cheers, Tsjerk On Oct 25, 2010 7:47 AM, Chih-Ying Lin chihying2...@gmail.com wrote: Hi g_rmsf -f abc.xtc -s abc.tpr -res -o abcrmsf.xvg *-[no]res* bool no Calculate averages for each residue abcrmsf.xvg = average over time for each residue? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_rmsf -res = does Gromacs do average over time for each residue ?
Hi g_rmsf -f abc.xtc -s abc.tpr -res -o abcrmsf.xvg From manual = it saysCalculate averages for each residue = does Gromacs do average over time for each residue ? = however, the results did not show difference with and without -res Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_rmsf -res = does Gromacs do average over time for each residue ?
Chih-Ying Lin wrote: Hi g_rmsf -f abc.xtc -s abc.tpr -res -o abcrmsf.xvg From manual = it saysCalculate averages for each residue = does Gromacs do average over time for each residue ? The average is done over time and over the atoms in the residue. = however, the results did not show difference with and without -res I doubt that. Without -res, you get RMSF per atom. With -res, you get RMSF per residue. The output is inherently (and necessarily) different. -Justin Thank you Lin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_rmsf -res = what does this function work?
Hi From Manual http://manual.gromacs.org/current/online/g_rmsf.html g_rmsf = optiontypedefaultdescription -[no]res bool noCalculate averages for each residue what does this function work? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_rmsf -res = what does this function work?
Chih-Ying Lin wrote: Hi From Manual http://manual.gromacs.org/current/online/g_rmsf.html g_rmsf = optiontypedefaultdescription -[no]res bool noCalculate averages for each residue what does this function work? Looking into the source code will answer this. -Justin Thank you Lin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_rmsf -res yes ? = should I type yes to activate the average-function ?
Hi g_rmsf -res yes ? g_rmsf -res no ? should I type yes to activate the average-function? As i tested g_rmsf -res, the average is not over time and not over the atoms in the residue. Anyway, how to activate the average function ? Thank you Lin Chih-Ying Lin wrote: Hi g_rmsf -f abc.xtc -s abc.tpr -res -o abcrmsf.xvg From manual = it saysCalculate averages for each residue = does Gromacs do average over time for each residue ? The average is done over time and over the atoms in the residue. = however, the results did not show difference with and without -res I doubt that. Without -res, you get RMSF per atom. With -res, you get RMSF per residue. The output is inherently (and necessarily) different. -Justin Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_rmsf -res yes ? = should I type yes to activate the average-function ?
Chih-Ying Lin wrote: Hi g_rmsf -res yes ? g_rmsf -res no ? should I type yes to activate the average-function? No. The command is either g_rmsf or g_rmsf -res. There is no yes or no required. As i tested g_rmsf -res, the average is not over time and not over the atoms in the residue. You will not get a plot over time. The calculation is done over time, but only the final result is plotted. If you have a plot of RMSF vs. residue, then averaging has been done over all the frames supplied, and over all the atoms in each residue. Unless you can prove that something has not been done correctly, then there is no need to repeatedly post the same question. -Justin Anyway, how to activate the average function ? Thank you Lin Chih-Ying Lin wrote: Hi g_rmsf -f abc.xtc -s abc.tpr -res -o abcrmsf.xvg From manual = it saysCalculate averages for each residue = does Gromacs do average over time for each residue ? The average is done over time and over the atoms in the residue. = however, the results did not show difference with and without -res I doubt that. Without -res, you get RMSF per atom. With -res, you get RMSF per residue. The output is inherently (and necessarily) different. -Justin Thank you Lin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_rmsf = average over # of time frames ???
Hi
From source code = gmx_rmsf.c
g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard ,
deviation) of atomic positions ,
if (devfn) {
/* Calculate RMS Deviation */
for(i=0;(iisize);i++) {
aid = index[i];
for(d=0;(dDIM);d++) {
rmsd_x[i][d] += sqr(x[aid][d]-xref[aid][d]);
}
}
}
count += 1.0;
rmsf[i] = (rmsd_x[i][XX]+rmsd_x[i][YY]+rmsd_x[i][ZZ])/count;
Therefore, g_rmsf is the average of structure deviation over the time
frames.
However, I issued the commands ( C-alpha is selected )
g_rmsf -f abc.xtc -b 0 -e 100 -s abc-crystal.tpr -o RMSF-abc-0th-100th.xvg
g_rmsf -f abc.xtc -b 100 -e 200 -s abc-crystal.tpr -o
RMSF-abc-100th-200th.xvg
g_rmsf -f abc.xtc -b 200 -e 300 -s abc-crystal.tpr -o
RMSF-abc-200th-300th.xvg
g_rmsf -f abc.xtc -b 300 -e 400 -s abc-crystal.tpr -o
RMSF-abc-300th-400th.xvg
g_rmsf -f abc.xtc -b 400 -e 500 -s abc-crystal.tpr -o
RMSF-abc-400th-500th.xvg
g_rmsf -f abc.xtc -b 500 -e 600 -s abc-crystal.tpr -o
RMSF-abc-500th-600th.xvg
g_rmsf -f abc.xtc -b 600 -e 700 -s abc-crystal.tpr -o
RMSF-abc-600th-700th.xvg
g_rmsf -f abc.xtc -b 700 -e 800 -s abc-crystal.tpr -o
RMSF-abc-700th-800th.xvg
g_rmsf -f abc.xtc -b 800 -e 900 -s abc-crystal.tpr -o
RMSF-abc-800th-900th.xvg
g_rmsf -f abc.xtc -b 900 -e 1000 -s abc-crystal.tpr -o
RMSF-abc-900th-1000th.xvg
Also, ( C-alpha is selected )
g_rmsf -f abc.xtc -b 0 -e 1000 -s abc-crystal.tpr -o RMSF-abc-0th-1000th.xvg
Then I ploted,
RMSF-abc-0th-100th.xvg
RMSF-abc-100th-200th.xvg
RMSF-abc-200th-300th.xvg
RMSF-abc-300th-400th.xvg
RMSF-abc-400th-500th.xvg
RMSF-abc-500th-600th.xvg
RMSF-abc-600th-700th.xvg
RMSF-abc-700th-800th.xvg
RMSF-abc-800th-900th.xvg
RMSF-abc-900th-1000th.xvg
Also, I ploted
RMSF-abc-0th-1000th.xvg
The PLOT RMSF-abc-0th-1000th.xvg has all RMSF-Values much higher than those
from RMSF-abc-0th-100th.xvg / RMSF-abc-100th-200th.xvg
/ RMSF-abc-200th-300th.xvg / .. / RMSF-abc-900th-1000th.xvg...
It does not make sense... I supposed.
Did I misunderstand something ?
THank you
Lin
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_rmsf -res = average over time for each residue?
Hi g_rmsf -f abc.xtc -s abc.tpr -res -o abcrmsf.xvg *-[no]res* bool no Calculate averages for each residue abcrmsf.xvg = average over time for each residue? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_rmsf
Hi, I am running an npt simulation for a protein in water. For more than 50% of the residues the backbone atoms have been restrained by applying posrestraints. I ran g_rmsf to check if the pos-restraints were working well. When I do this selecting 'backbone' from the groups menu, my rmsf file gives 'nan' for certain residues: # This file was created Sat Jul 17 13:40:21 2010 # by the following command: # ../../gromacsnew/bin/g_rmsf -f npt1.cpt -s npt1.tpr -b 0 -e 80 -o rmsf2_npt1.xvg -od rmsd2_npt1.xvg -res # # g_rmsf is part of G R O M A C S: # # GROup of MAchos and Cynical Suckers # @title RMS fluctuation @xaxis label Residue @yaxis label (nm) @TYPE xy 1 nan 2 nan 3 0.0002 4 0. 5 nan 1 0.0002 2 nan 3 nan 4 0.0001 5 nan 6 0.0001 7 nan 8 nan 9 0. 10 0.0002 11 nan 12 nan 13 nan 14 nan 15 0. 16 nan 17 0.0001 18 0.0002 Does this mean that the simulations are not working properly? Does this problem occur frequently due to the way the simulation parameters haev been set? Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rmsf
Hi Pooja, Try to get a grip on the file types and what they contain. A .cpt file is a checkpoint file containing a single configuration. Not much fluctuation to expect there. This sort of analysis only makes sense for a trajectory, or at least an ensemble of structures. Try the .xtc or the .trr file. Cheers, Tsjerk On Sat, Jul 17, 2010 at 7:55 PM, Sai Pooja saipo...@gmail.com wrote: Hi, I am running an npt simulation for a protein in water. For more than 50% of the residues the backbone atoms have been restrained by applying posrestraints. I ran g_rmsf to check if the pos-restraints were working well. When I do this selecting 'backbone' from the groups menu, my rmsf file gives 'nan' for certain residues: # This file was created Sat Jul 17 13:40:21 2010 # by the following command: # ../../gromacsnew/bin/g_rmsf -f npt1.cpt -s npt1.tpr -b 0 -e 80 -o rmsf2_npt1.xvg -od rmsd2_npt1.xvg -res # # g_rmsf is part of G R O M A C S: # # GROup of MAchos and Cynical Suckers # @ title RMS fluctuation @ xaxis label Residue @ yaxis label (nm) @TYPE xy 1 nan 2 nan 3 0.0002 4 0. 5 nan 1 0.0002 2 nan 3 nan 4 0.0001 5 nan 6 0.0001 7 nan 8 nan 9 0. 10 0.0002 11 nan 12 nan 13 nan 14 nan 15 0. 16 nan 17 0.0001 18 0.0002 Does this mean that the simulations are not working properly? Does this problem occur frequently due to the way the simulation parameters haev been set? Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rmsf -res
Hi Tsjerk, thank you for your answer. Actually, for the initial structure, I took the values of the B factor, and calculated the mean square displacement per atom. This is what I meant by saying RMSF of initial structure. Anyway, thanks for the explanation. But I have another question: I need to take 3 structures and make an average structure of these 3. Is there a way to do it with gromacs? Cheers, Carla On Thu, Jun 10, 2010 at 12:15 PM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi Carla, On Thu, Jun 10, 2010 at 12:03 PM, Carla Jamous carlajam...@gmail.com wrote: Hi Everyone, please I have a question concerning g_rmsf. I need to compare the RMSF from my initial structure to the RMSF of my average structure. Single structures (initial c.q. average) do not have an RMSF. When I did g_rmsf -s .tpr -f .xtc -n .ndx -b xx -e yy -o rmsf or g_rmsf -s .tpr -f .xtc -n .ndx -b xx -e yy -res -o rmsf This is not what you did. Please copy/paste command lines. I got the same result, when choosing C-alpha for root mean square calculation. Sure, when selecting C-alphas, averaging the RMSF per residue (sum_over_calphas_in_residue/number_of_calphas_in_residue) will evidently be identical to calculating the RMSF on an atom basis for each Calpha. So please can anyone explain how can I get the average per residue over a period of time? Select 'protein' (and use the -res flag). Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rmsf -res
Hi, yes it can be done with g_covar, but such an average structure is often of little physical significace. Imagine for instance the acerage structure of a rotating methyle group (it's a bunch of atoms on a line). Erik Carla Jamous skrev: Hi Tsjerk, thank you for your answer. Actually, for the initial structure, I took the values of the B factor, and calculated the mean square displacement per atom. This is what I meant by saying RMSF of initial structure. Anyway, thanks for the explanation. But I have another question: I need to take 3 structures and make an average structure of these 3. Is there a way to do it with gromacs? Cheers, Carla On Thu, Jun 10, 2010 at 12:15 PM, Tsjerk Wassenaar tsje...@gmail.com mailto:tsje...@gmail.com wrote: Hi Carla, On Thu, Jun 10, 2010 at 12:03 PM, Carla Jamous carlajam...@gmail.com mailto:carlajam...@gmail.com wrote: Hi Everyone, please I have a question concerning g_rmsf. I need to compare the RMSF from my initial structure to the RMSF of my average structure. Single structures (initial c.q. average) do not have an RMSF. When I did g_rmsf -s .tpr -f .xtc -n .ndx -b xx -e yy -o rmsf or g_rmsf -s .tpr -f .xtc -n .ndx -b xx -e yy -res -o rmsf This is not what you did. Please copy/paste command lines. I got the same result, when choosing C-alpha for root mean square calculation. Sure, when selecting C-alphas, averaging the RMSF per residue (sum_over_calphas_in_residue/number_of_calphas_in_residue) will evidently be identical to calculating the RMSF on an atom basis for each Calpha. So please can anyone explain how can I get the average per residue over a period of time? Select 'protein' (and use the -res flag). Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rmsf -res
Please does anyone know how is calculated the B factor in gromacs? What is the formula that gives the B factor with the average coordinates with g_rmsf? Carla On Fri, Jun 11, 2010 at 10:53 AM, Erik Marklund er...@xray.bmc.uu.sewrote: Hi, yes it can be done with g_covar, but such an average structure is often of little physical significace. Imagine for instance the acerage structure of a rotating methyle group (it's a bunch of atoms on a line). Erik Carla Jamous skrev: Hi Tsjerk, thank you for your answer. Actually, for the initial structure, I took the values of the B factor, and calculated the mean square displacement per atom. This is what I meant by saying RMSF of initial structure. Anyway, thanks for the explanation. But I have another question: I need to take 3 structures and make an average structure of these 3. Is there a way to do it with gromacs? Cheers, Carla On Thu, Jun 10, 2010 at 12:15 PM, Tsjerk Wassenaar tsje...@gmail.commailto: tsje...@gmail.com wrote: Hi Carla, On Thu, Jun 10, 2010 at 12:03 PM, Carla Jamous carlajam...@gmail.com mailto:carlajam...@gmail.com wrote: Hi Everyone, please I have a question concerning g_rmsf. I need to compare the RMSF from my initial structure to the RMSF of my average structure. Single structures (initial c.q. average) do not have an RMSF. When I did g_rmsf -s .tpr -f .xtc -n .ndx -b xx -e yy -o rmsf or g_rmsf -s .tpr -f .xtc -n .ndx -b xx -e yy -res -o rmsf This is not what you did. Please copy/paste command lines. I got the same result, when choosing C-alpha for root mean square calculation. Sure, when selecting C-alphas, averaging the RMSF per residue (sum_over_calphas_in_residue/number_of_calphas_in_residue) will evidently be identical to calculating the RMSF on an atom basis for each Calpha. So please can anyone explain how can I get the average per residue over a period of time? Select 'protein' (and use the -res flag). Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_rmsf -res
Hi Everyone, please I have a question concerning g_rmsf. I need to compare the RMSF from my initial structure to the RMSF of my average structure. To do so, I need to calculate the average per residue. When I did g_rmsf -s .tpr -f .xtc -n .ndx -b xx -e yy -o rmsf or g_rmsf -s .tpr -f .xtc -n .ndx -b xx -e yy -res -o rmsf I got the same result, when choosing C-alpha for root mean square calculation. So please can anyone explain how can I get the average per residue over a period of time? Thanks, Carla -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rmsf -res
Hi Carla, On Thu, Jun 10, 2010 at 12:03 PM, Carla Jamous carlajam...@gmail.com wrote: Hi Everyone, please I have a question concerning g_rmsf. I need to compare the RMSF from my initial structure to the RMSF of my average structure. Single structures (initial c.q. average) do not have an RMSF. When I did g_rmsf -s .tpr -f .xtc -n .ndx -b xx -e yy -o rmsf or g_rmsf -s .tpr -f .xtc -n .ndx -b xx -e yy -res -o rmsf This is not what you did. Please copy/paste command lines. I got the same result, when choosing C-alpha for root mean square calculation. Sure, when selecting C-alphas, averaging the RMSF per residue (sum_over_calphas_in_residue/number_of_calphas_in_residue) will evidently be identical to calculating the RMSF on an atom basis for each Calpha. So please can anyone explain how can I get the average per residue over a period of time? Select 'protein' (and use the -res flag). Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rmsf over time windows
Hi Giordano, Do you have a conformational change? If you consider unidirectional motion, in one or N coordinates alike, you would expect just what you see for the fluctuations. In fact, it's not really fluctuation then. 10 ns is also pretty short for a simulation of a protein. It's likely that you're analyzing relaxation from the starting structure. Cheers, Tsjerk On Tue, Oct 7, 2008 at 8:03 PM, giordano mancini [EMAIL PROTECTED] wrote: Hi all, I have the following problem: I have a simulation of 10 ns of a protein in water. I have extracted the protein trajectory with trjconv -pbc nojump and the fitted it to a reference structure with trjconv -fit rot+trans. If I run g_rmsf -nofit over two consecutive chunks of 5 ns i get very similar rmsf values (so the fluctuations are are the same in the 2 time windows). However if I run g_rmsf over the whole trajectory i get much higher values of rmsf (up to 0.1 - 0.15 nm). The difference become higher if use 4 windows of 2.5 ns each (i.e. the rmsf over 2.5 ns are smaller). I think there's something wrong with the reference structure which is different in the various cases so that with shorter trajectories the std dev is smaller; however I always use the same .gro (or tpr). May be are the -b and -e flags? Use of tpr/gro reference, fit with g_rmsf, calpha or backbone, or -res option does not change things. I have tried with gromacs 3.3.1 and 3.3.3 Here 's my complete syntax: $ trjconv -s box.gro -f nojump.xtc -n index.ndx -o nj -pbc nojump $ trjconv -s box.gro -f nj.xtc -n index -fit rot+trans -o fitted $ g_rmsf -s box.gro -f fitted -n index -o rmsf$start -b $start -e $end for chuncks $ g_rmsf -s box.gro -f fitted -n index -o rmsf thanks for your help giordnao mancini ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rmsf over time windows
Hi Giordano, I agree that 10 ns are a short sampling but the total simulation time is 15 ns + 2 ns I used to reach 298K; Whether that's enough is largely dependent on the size of your protein You should check whether you went beyond relaxation by inspecting the cosine content of the first few eigenvectors. since the rmsd was almost flat in this 10 ns I was hoping that results were not influenced by relaxation. This by itself does not mean anything. If it levels off at 0.1 nm, okay, that's pretty good, but the further you go, the more possibilities you have for getting a certain RMSD. It's a distance measure. Being at 10 cm distance from you will make it easy to localize me, but if I'm at 10 miles, you wouldn't now where to search. I could well go 10 miles and then start following a circle, and you'd argue, based on the distance, that I'd stopped moving! Maybe g_rmsf calculates fluctuations from the average structure in a certain time window and not from the reference or starting frame (and it is my fault not to have read the program help well). In this case my results would make sense. That is indeed the case. And if your system had converged, there wouldn't be a difference between the average structures from subtrajectories A and B. The RMSF is only defined about the mean structure. You don't want to go into non-central moments. If you have the average structure for the whole trajectory, you can use it as the reference to calculate the RMSF. I believe that g_rmsf has an option to use deviations from the reference rather than from the calculated average structure. Hope it helps, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rmsf over time windows
Hi Tsjerk, thanks for your reply. I have inspected a trajectory movie with vmd and made a superimposition of the starting and last configuration with the reference structure (which is just the the crystallographic pdb) and (inspecting them visually), I do not see any significant conformational change (apart in one subdomain,but this is expected). I agree that 10 ns are a short sampling but the total simulation time is 15 ns + 2 ns I used to reach 298K; since the rmsd was almost flat in this 10 ns I was hoping that results were not influenced by relaxation. Maybe g_rmsf calculates fluctuations from the average structure in a certain time window and not from the reference or starting frame (and it is my fault not to have read the program help well). In this case my results would make sense. giordano Tsjerk Wassenaar wrote: Hi Giordano, Do you have a conformational change? If you consider unidirectional motion, in one or N coordinates alike, you would expect just what you see for the fluctuations. In fact, it's not really fluctuation then. 10 ns is also pretty short for a simulation of a protein. It's likely that you're analyzing relaxation from the starting structure. Cheers, Tsjerk ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rmsf over time windows
Hi Tsjerk Whether that's enough is largely dependent on the size of your protein You should check whether you went beyond relaxation by inspecting the cosine content of the first few eigenvectors. This by itself does not mean anything. If it levels off at 0.1 nm, okay, that's pretty good, but the further you go, the more possibilities you have for getting a certain RMSD. It's a distance measure. Being at 10 cm distance from you will make it easy to localize me, but if I'm at 10 miles, you wouldn't now where to search. I could well go 10 miles and then start following a circle, and you'd argue, based on the distance, that I'd stopped moving! Ok; i have not checked it still; I wanted to check deviation and fluctuations first to see if some unexpected/abnormal behavior in the protein. but now I got your point about rmsd and relaxation That is indeed the case. And if your system had converged, there wouldn't be a difference between the average structures from subtrajectories A and B. The RMSF is only defined about the mean structure. You don't want to go into non-central moments. If you have the average structure for the whole trajectory, you can use it as the reference to calculate the RMSF. I believe that g_rmsf has an option to use deviations from the reference rather than from the calculated average structure. Actually the manual says it (option -od?). My fault. Anyway it has been useful to think about it. Hope it helps, It did; thank you. cheeres giordano ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_rmsf over time windows
Hi all, I have the following problem: I have a simulation of 10 ns of a protein in water. I have extracted the protein trajectory with trjconv -pbc nojump and the fitted it to a reference structure with trjconv -fit rot+trans. If I run g_rmsf -nofit over two consecutive chunks of 5 ns i get very similar rmsf values (so the fluctuations are are the same in the 2 time windows). However if I run g_rmsf over the whole trajectory i get much higher values of rmsf (up to 0.1 - 0.15 nm). The difference become higher if use 4 windows of 2.5 ns each (i.e. the rmsf over 2.5 ns are smaller). I think there's something wrong with the reference structure which is different in the various cases so that with shorter trajectories the std dev is smaller; however I always use the same .gro (or tpr). May be are the -b and -e flags? Use of tpr/gro reference, fit with g_rmsf, calpha or backbone, or -res option does not change things. I have tried with gromacs 3.3.1 and 3.3.3 Here 's my complete syntax: $ trjconv -s box.gro -f nojump.xtc -n index.ndx -o nj -pbc nojump $ trjconv -s box.gro -f nj.xtc -n index -fit rot+trans -o fitted $ g_rmsf -s box.gro -f fitted -n index -o rmsf$start -b $start -e $end for chuncks $ g_rmsf -s box.gro -f fitted -n index -o rmsf thanks for your help giordnao mancini ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rmsf
sudheer babu wrote: Hi, I would like to calculate B-factor of protein, so I performed command like this g_rmsf -f .xtc -s .tpr -res -o fluctuate.xvg -od devi.xvg it has run without error.Now i am bit doubting that which .xvg file have to take for plot B-factor values? I think you have not specified the correct options. Check g_rmsf -h and read about the -oq option. -Justin B-factor is nothing but thermal devation of atoms. I think, I should take dev.xvg for plotting B-factor values, if it is coorect, then what' s the need for producing fluctuate.xvg? may be this is trivial question. Could anyone help me pls. Thanks alot in advance ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_rmsf
Dear gmx users, I have a basic query. With respect to which structure are the rmsf values calculated per each atom? is it w.r.t average structure of the protein or the reference structure that we provide using -s option? I dont find any explanation of the output generated using g_rmsf. Please make this clear. Thanks!! Swapna On Mon, Apr 7, 2008 at 5:06 AM, Maik Goette [EMAIL PROTECTED] wrote: QL, 1. Yes. I'd use version a) because of, the less dummies, the better. 2. Yes 3. Of course, charges have to vanish for dummies, too. Keep the bonded terms. If not, your dummies will diffuse away. Yes, your assumption about dummies is right. Actually, I won't use this system for your first perturbation. Take something simpler. Second, as indicated by point 3, you will have to tackle a disappearing netto charge of -1 (depending on the pH of course). This usually is a problem. There were discussions of PME being problematic here. Morphing an ion to counter that charge difference is possible. However, I think this would lead to a very bad equilibrated system and no reasonable results. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ friendli wrote: Dear Gmx users, I am calculating the mutation free energy from amino acid Asp to Asn as a test job for my practice. I have some questions about setting up the topology file. 1, from Asp to Asn mutation, the -CH2-COOH changes to -CH2-CO-NH2 or simply -OH to -NH2. In topology, O - N. What about the hydrogens, do I need one or two dummy(DUM) atoms? a), DUM - H ; H(of OH) - H(of NH2) b), DUM - H(of NH2); DUM - H(of NH2); H(of OH) to DUM a) or b) should I use? 2, I need to provide the coordinates for the dummy atoms in the .gro file(Asp), right? since otherwise the # of atoms in .top and .gro will mismatch. 3, from the tutorial(methane) I read, the masses of the dummy atom keeps like real atom and the C6 and C12 changes to zero in [atomtypes] to vanish the nonbonded interactions. How to deal with the bonds and the charges for dummy atoms? bonded interactions? I think I am a bit confused by the definition of the dummy atom. I understanding is a dummy atom is a atoms with same mass but no interaction with all other atoms. Is that right? thanks for help and suggestions are appreciate. QL ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- The logic of life lies exclusively neither in the most incredible detail, nor in the most sweeping synopsis. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rmsf
SWAPNA wrote: Dear gmx users, I have a basic query. With respect to which structure are the rmsf values calculated per each atom? is it w.r.t average structure of the protein or the reference structure that we provide using -s option? I dont find any explanation of the output generated using g_rmsf. Please make this clear. Look at g_rmsf -h because the reference structure is explained there. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rmsf fitting
tangxuan wrote: Hi Tsjerk, Yes, you are right. My protein has multiple subunits. I have a original tpr file ref1.tpr which is the input to start the simulation. I have checked the protein structure in this tpr file. The subunits have no contact each other obviously, without jump in them and I can not see an intact protein. However, the structure in the frames shows that there is a whole protein with jump. Therefore, the structure in the tpr file is different from the structure in the first frame. The simulation is 30ns long and I am trying to calculate the rmsf between 20ns and 30ns. I removed the jumps in whole simulation(trjconv -f .xtc(.trr) -s ref1.tpr -pbc nojump) first and got the nojump xtc file between 20ns and 30ns. The main difference between is the tpr file at 20ns(ref20.tpr) i used and two ways I have used to get it: 1) used ref1.tpr and original trr file to get a tpr file at 20ns ref20.tpr by tpbconv. 2) used ref1.tpr and nojump trr file to get a tpr file at 20ns ref20.tpr by tpbconv. then g_rmsf -f .xtc (nojump) -s ref20.tpr -res is used to calculate the rmsf. I take out part of the result below and the results are from two methods for same subunit. What happens whan you overlay the two reference structures using g_confrms? Is it high RMSD? Both reference structures and trajectories should be jump-free. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rmsf fitting
Hi Tang, The subunits have no contact each other obviously, without jump in them and I can not see an intact protein. Please be more clear and try to write full, correct sentences. I suppose you mean that the subunits are separated at start, so there has been a jump in the setup stage. However, the structure in the frames shows that there is a whole protein with jump. Therefore, the structure in the tpr file is different from the structure in the first frame. So (one of the) subunits occasionally jump(s) back and make the molecule whole. The simulation is 30ns long and I am trying to calculate the rmsf between 20ns and 30ns. I removed the jumps in whole simulation(trjconv -f .xtc(.trr) -s ref1.tpr -pbc nojump) first and got the nojump xtc file between 20ns and 30ns. Assuming that ref1.tpr corresponds to your starting structure, which has the subunits separated, this means that you end up with a trajectory which has the subunits separated consistently. The main difference between is the tpr file at 20ns(ref20.tpr) i used and two ways I have used to get it: 1) used ref1.tpr and original trr file to get a tpr file at 20ns ref20.tpr by tpbconv. This reference may be of the correct complex (check it). 2) used ref1.tpr and nojump trr file to get a tpr file at 20ns ref20.tpr by tpbconv. And this will have the subunits separated. then g_rmsf -f .xtc (nojump) -s ref20.tpr -res is used to calculate the rmsf. So the answer is in the structures (jump/nojump) and not in the way g_rmsf performs the fit and calculates the rmsf. Try to make this line of thinking your own and check the structures (references/selected frames from trajectories) first whenever you encounter problems like this. This issue has also been covered before, and I recall having posted a message on this list regarding the correct use of references, fitting and -pbc options using trjconv, which may be useful to you. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rmsf fitting
Thanks for your detailed explanation. Sorry for my words and I wrote them in a hurry without careful check. In fact, I can not see a whole protein in ref1.tpr and part of subunits are out of box. I do not know if this can be called jump. Tang Tsjerk Wassenaar wrote: Hi Tang, The subunits have no contact each other obviously, without jump in them and I can not see an intact protein. Please be more clear and try to write full, correct sentences. I suppose you mean that the subunits are separated at start, so there has been a jump in the setup stage. However, the structure in the frames shows that there is a whole protein with jump. Therefore, the structure in the tpr file is different from the structure in the first frame. So (one of the) subunits occasionally jump(s) back and make the molecule whole. The simulation is 30ns long and I am trying to calculate the rmsf between 20ns and 30ns. I removed the jumps in whole simulation(trjconv -f .xtc(.trr) -s ref1.tpr -pbc nojump) first and got the nojump xtc file between 20ns and 30ns. Assuming that ref1.tpr corresponds to your starting structure, which has the subunits separated, this means that you end up with a trajectory which has the subunits separated consistently. The main difference between is the tpr file at 20ns(ref20.tpr) i used and two ways I have used to get it: 1) used ref1.tpr and original trr file to get a tpr file at 20ns ref20.tpr by tpbconv. This reference may be of the correct complex (check it). 2) used ref1.tpr and nojump trr file to get a tpr file at 20ns ref20.tpr by tpbconv. And this will have the subunits separated. then g_rmsf -f .xtc (nojump) -s ref20.tpr -res is used to calculate the rmsf. So the answer is in the structures (jump/nojump) and not in the way g_rmsf performs the fit and calculates the rmsf. Try to make this line of thinking your own and check the structures (references/selected frames from trajectories) first whenever you encounter problems like this. This issue has also been covered before, and I recall having posted a message on this list regarding the correct use of references, fitting and -pbc options using trjconv, which may be useful to you. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rmsf fitting
See http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions On Jan 4, 2008 11:20 AM, tangxuan [EMAIL PROTECTED] wrote: Thanks for your detailed explanation. Sorry for my words and I wrote them in a hurry without careful check. In fact, I can not see a whole protein in ref1.tpr and part of subunits are out of box. I do not know if this can be called jump. Tang Tsjerk Wassenaar wrote: Hi Tang, The subunits have no contact each other obviously, without jump in them and I can not see an intact protein. Please be more clear and try to write full, correct sentences. I suppose you mean that the subunits are separated at start, so there has been a jump in the setup stage. However, the structure in the frames shows that there is a whole protein with jump. Therefore, the structure in the tpr file is different from the structure in the first frame. So (one of the) subunits occasionally jump(s) back and make the molecule whole. The simulation is 30ns long and I am trying to calculate the rmsf between 20ns and 30ns. I removed the jumps in whole simulation(trjconv -f .xtc(.trr) -s ref1.tpr -pbc nojump) first and got the nojump xtc file between 20ns and 30ns. Assuming that ref1.tpr corresponds to your starting structure, which has the subunits separated, this means that you end up with a trajectory which has the subunits separated consistently. The main difference between is the tpr file at 20ns(ref20.tpr) i used and two ways I have used to get it: 1) used ref1.tpr and original trr file to get a tpr file at 20ns ref20.tpr by tpbconv. This reference may be of the correct complex (check it). 2) used ref1.tpr and nojump trr file to get a tpr file at 20ns ref20.tpr by tpbconv. And this will have the subunits separated. then g_rmsf -f .xtc (nojump) -s ref20.tpr -res is used to calculate the rmsf. So the answer is in the structures (jump/nojump) and not in the way g_rmsf performs the fit and calculates the rmsf. Try to make this line of thinking your own and check the structures (references/selected frames from trajectories) first whenever you encounter problems like this. This issue has also been covered before, and I recall having posted a message on this list regarding the correct use of references, fitting and -pbc options using trjconv, which may be useful to you. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_rmsf fitting
Hi, Does anyone know how fitting step works in detail when running g_rmsf? When I used two different tpr files with same protein structure but different atoms position, the result is very different. Can you explain this ? many thanks! Tang ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rmsf fitting
Hi Tang, It's just the general case of least-squares fitting: 1. Bring centres of geometry/mass to origin 2. Calculate (mass-weighted) rotation matrix 3. Rotate structure (4. Calculate squared displacements) But what do you mean with 'very different'. Can you provide an example? What command line did you use? Do you have multiple subunits and have jumps over PBC between the two reference structures? Cheers, Tsjerk On Jan 3, 2008 3:37 PM, tangxuan [EMAIL PROTECTED] wrote: Hi, Does anyone know how fitting step works in detail when running g_rmsf? When I used two different tpr files with same protein structure but different atoms position, the result is very different. Can you explain this ? many thanks! Tang ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rmsf fitting
Hi Tsjerk, Yes, you are right. My protein has multiple subunits. I have a original tpr file ref1.tpr which is the input to start the simulation. I have checked the protein structure in this tpr file. The subunits have no contact each other obviously, without jump in them and I can not see an intact protein. However, the structure in the frames shows that there is a whole protein with jump. Therefore, the structure in the tpr file is different from the structure in the first frame. The simulation is 30ns long and I am trying to calculate the rmsf between 20ns and 30ns. I removed the jumps in whole simulation(trjconv -f .xtc(.trr) -s ref1.tpr -pbc nojump) first and got the nojump xtc file between 20ns and 30ns. The main difference between is the tpr file at 20ns(ref20.tpr) i used and two ways I have used to get it: 1) used ref1.tpr and original trr file to get a tpr file at 20ns ref20.tpr by tpbconv. 2) used ref1.tpr and nojump trr file to get a tpr file at 20ns ref20.tpr by tpbconv. then g_rmsf -f .xtc (nojump) -s ref20.tpr -res is used to calculate the rmsf. I take out part of the result below and the results are from two methods for same subunit. 1) 62 0.1937 63 0.2319 64 0.2058 65 0.2027 66 0.1785 67 0.1625 68 0.1641 69 0.1683 70 0.1402 71 0.1353 72 0.1122 73 0.0984 74 0.0935 75 0.1094 76 0.0797 77 0.1318 78 0.0928 79 0.1255 80 0.1251 81 0.1525 82 0.1716 83 0.1509 84 0.1333 85 0.0911 86 0.0984 87 0.0642 88 0.0862 89 0.0648 90 0.0793 91 0.0918 92 0.1218 93 0.1318 94 0.1609 95 0.1717 96 0.1812 97 0.1569 98 0.1683 99 0.1495 2) 62 0.0843 63 0.0946 64 0.0801 65 0.0652 66 0.0801 67 0.0605 68 0.0728 69 0.0733 70 0.0561 71 0.0559 72 0.0628 73 0.0552 74 0.0613 75 0.0758 76 0.0639 77 0.1172 78 0.0677 79 0.0877 80 0.0981 81 0.1313 82 0.1490 83 0.1460 84 0.1133 85 0.0947 86 0.0761 87 0.0602 88 0.0677 89 0.0587 90 0.0530 91 0.0545 92 0.0647 93 0.0451 94 0.0560 95 0.0541 96 0.0572 97 0.0486 98 0.0535 99 0.0459 Thanks Tang Tsjerk Wassenaar wrote: Hi Tang, It's just the general case of least-squares fitting: 1. Bring centres of geometry/mass to origin 2. Calculate (mass-weighted) rotation matrix 3. Rotate structure (4. Calculate squared displacements) But what do you mean with 'very different'. Can you provide an example? What command line did you use? Do you have multiple subunits and have jumps over PBC between the two reference structures? Cheers, Tsjerk On Jan 3, 2008 3:37 PM, tangxuan [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Hi, Does anyone know how fitting step works in detail when running g_rmsf? When I used two different tpr files with same protein structure but different atoms position, the result is very different. Can you explain this ? many thanks! Tang ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_rmsf Segmentation fault
To the gmx-users, When executing: g_rmsf -f traj.trr -s topol.tpr -o rmsf.xvg -aniso I get the following error after running through all the frames: Segmentations fault If I don't include the aniso flag I don't get an segfault. Can anyone explain to me, why it is not working with the aniso flag? Kind regards, Tommy Tommy Carstensen UCD School of Biomolecular and Biomedical Sciences Conway Institute University College Dublin Dublin 4, Ireland http://enzyme.ucd.ie/group_members/tommy ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rmsf Segmentation fault
Tommy Carstensen wrote: To the gmx-users, When executing: g_rmsf -f traj.trr -s topol.tpr -o rmsf.xvg -aniso I get the following error after running through all the frames: Segmentations fault If I don't include the aniso flag I don't get an segfault. Can anyone explain to me, why it is not working with the aniso flag? probably a bug. maybe it works if you input a pdbfile with reference B values. Anyway you're welcome to submit a bugzilla, please upload input files to reproduce the problem. Kind regards, Tommy Tommy Carstensen UCD School of Biomolecular and Biomedical Sciences Conway Institute University College Dublin Dublin 4, Ireland http://enzyme.ucd.ie/group_members/tommy ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rmsf and pbc
I tried trjconv -pbc nojump to the whole protein and then calculated the rmsf of the subunits. This method seems good to some separate subunits, but other separate subunits still have strange high rmsf values. I try trjconv -pbc mol too, and i have got same results. In this simulation,the subunits are separate in the first frame. Do you have any other methods to solve this problem? On Tue, 2007-10-23 at 17:18 +0200, David van der Spoel wrote: tangxuan wrote: Mark,thanks for your reply. I am not sure what happened and I can show you the error message, Group 101 ( chK_chM) has 4070 elements Group 102 ( chM_chO) has 4070 elements Group 103 ( chO_chI) has 4070 elements Group 104 ( chJ_chL) has 4070 elements Group 105 ( chL_chN) has 4070 elements Group 106 ( chN_chP) has 4070 elements Group 107 ( chP_chJ) has 4070 elements Select a group: 22 Selected 22: 'chC' Reading frame 1 time 20001.000 Segmentation fault [miro:~/rubisco-2/chlamy_wt] % more chlamy_wt.xtc Thanks. Tang jiaowei most likely the tpr and xtc files have different number of atoms. as for your original problem, try trjconv -pbc mol in version 3.3.2 On Wed, 2007-10-24 at 00:43 +1000, Mark Abraham wrote: tangxuan wrote: Dear all, The protein I am working on is rubisco, consisting of 8 identical large subunits and 8 identical small subunits. I try to calculate RMSF for each large subunits, but the rmsf values seems much large to some large subunits. So I check the first frame of the protein structutre, and I found that these large subunits having large rmsf values seems separate in the box. Then I tried to use trjconv -pbc nojump to remove the jump for each of them in the xtc file. When I use new xtc file and original tpr file to calculate the rmsf, it shows Segmentation fault error. This may be because the coordinators of atoms in the tpr file are very diffrent from that in the fist frame. Do you know how to solve this problem? GROMACS does an inexplicable segfault almost never. It's highly likely that either there's more of an error message than you've said, or that the problem is the result some catastrophic filesystem or OS issue. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_rmsf and pbc
Dear all, The protein I am working on is rubisco, consisting of 8 identical large subunits and 8 identical small subunits. I try to calculate RMSF for each large subunits, but the rmsf values seems much large to some large subunits. So I check the first frame of the protein structutre, and I found that these large subunits having large rmsf values seems separate in the box. Then I tried to use trjconv -pbc nojump to remove the jump for each of them in the xtc file. When I use new xtc file and original tpr file to calculate the rmsf, it shows Segmentation fault error. This may be because the coordinators of atoms in the tpr file are very diffrent from that in the fist frame. Do you know how to solve this problem? Thank you Tang Jiaowei ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rmsf and pbc
tangxuan wrote: Dear all, The protein I am working on is rubisco, consisting of 8 identical large subunits and 8 identical small subunits. I try to calculate RMSF for each large subunits, but the rmsf values seems much large to some large subunits. So I check the first frame of the protein structutre, and I found that these large subunits having large rmsf values seems separate in the box. Then I tried to use trjconv -pbc nojump to remove the jump for each of them in the xtc file. When I use new xtc file and original tpr file to calculate the rmsf, it shows Segmentation fault error. This may be because the coordinators of atoms in the tpr file are very diffrent from that in the fist frame. Do you know how to solve this problem? GROMACS does an inexplicable segfault almost never. It's highly likely that either there's more of an error message than you've said, or that the problem is the result some catastrophic filesystem or OS issue. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rmsf and pbc
Mark,thanks for your reply. I am not sure what happened and I can show you the error message, Group 101 ( chK_chM) has 4070 elements Group 102 ( chM_chO) has 4070 elements Group 103 ( chO_chI) has 4070 elements Group 104 ( chJ_chL) has 4070 elements Group 105 ( chL_chN) has 4070 elements Group 106 ( chN_chP) has 4070 elements Group 107 ( chP_chJ) has 4070 elements Select a group: 22 Selected 22: 'chC' Reading frame 1 time 20001.000 Segmentation fault [miro:~/rubisco-2/chlamy_wt] % more chlamy_wt.xtc Thanks. Tang jiaowei On Wed, 2007-10-24 at 00:43 +1000, Mark Abraham wrote: tangxuan wrote: Dear all, The protein I am working on is rubisco, consisting of 8 identical large subunits and 8 identical small subunits. I try to calculate RMSF for each large subunits, but the rmsf values seems much large to some large subunits. So I check the first frame of the protein structutre, and I found that these large subunits having large rmsf values seems separate in the box. Then I tried to use trjconv -pbc nojump to remove the jump for each of them in the xtc file. When I use new xtc file and original tpr file to calculate the rmsf, it shows Segmentation fault error. This may be because the coordinators of atoms in the tpr file are very diffrent from that in the fist frame. Do you know how to solve this problem? GROMACS does an inexplicable segfault almost never. It's highly likely that either there's more of an error message than you've said, or that the problem is the result some catastrophic filesystem or OS issue. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rmsf and pbc
tangxuan wrote: Mark,thanks for your reply. I am not sure what happened and I can show you the error message, Group 101 ( chK_chM) has 4070 elements Group 102 ( chM_chO) has 4070 elements Group 103 ( chO_chI) has 4070 elements Group 104 ( chJ_chL) has 4070 elements Group 105 ( chL_chN) has 4070 elements Group 106 ( chN_chP) has 4070 elements Group 107 ( chP_chJ) has 4070 elements Select a group: 22 Selected 22: 'chC' Reading frame 1 time 20001.000 Segmentation fault [miro:~/rubisco-2/chlamy_wt] % more chlamy_wt.xtc Thanks. Tang jiaowei most likely the tpr and xtc files have different number of atoms. as for your original problem, try trjconv -pbc mol in version 3.3.2 On Wed, 2007-10-24 at 00:43 +1000, Mark Abraham wrote: tangxuan wrote: Dear all, The protein I am working on is rubisco, consisting of 8 identical large subunits and 8 identical small subunits. I try to calculate RMSF for each large subunits, but the rmsf values seems much large to some large subunits. So I check the first frame of the protein structutre, and I found that these large subunits having large rmsf values seems separate in the box. Then I tried to use trjconv -pbc nojump to remove the jump for each of them in the xtc file. When I use new xtc file and original tpr file to calculate the rmsf, it shows Segmentation fault error. This may be because the coordinators of atoms in the tpr file are very diffrent from that in the fist frame. Do you know how to solve this problem? GROMACS does an inexplicable segfault almost never. It's highly likely that either there's more of an error message than you've said, or that the problem is the result some catastrophic filesystem or OS issue. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_rmsf and the -fit option , calculating average structures
I see to calculate the average structure of a protein in a trajectory minus any rotational + translational effects, using g_rmsf. Does the -fit option (default yes) eliminate rot + trans contributions? Or must one use trjconv first, to convert the trajectory to some reference frame eliminating the rot+trans, and then use g_rmsf on that new trajecotry??? Thanks, Arneh ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rmsf and the -fit option , calculating average structures
Arneh Babakhani wrote: I see to calculate the average structure of a protein in a trajectory minus any rotational + translational effects, using g_rmsf. Does the -fit option (default yes) eliminate rot + trans contributions? Yes, it will. If it can't rotate and translate, it's not much of a fit :-) Or must one use trjconv first, to convert the trajectory to some reference frame eliminating the rot+trans, and then use g_rmsf on that new trajecotry??? You could try it and see? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_rmsf -res bug
Hi all,
I was looking at the output of various g_rmsf runs, and came upon the fact that
the RMSF values obtained using -res and then choosing Mainchain (5)
for RMS calculation, were exactly the same as the RMSF values of
Mainchain Oxygen atoms obtained not using -res. I gave a look at the
code to see why this was the case, and discovered that the averaging
operation:
[src/tools/gmx_rmsf.c lines 355-356]
...
if (bRes) {
average_residues(rmsf,isize,index,w_rls,top.atoms);
...
is done before the rmsf array is filled with the values from the U
tensors. Thus the values output by g_rmsf are the RMSF values of the
last atom of each residue (and not the average of the residue), and in
the case of the Mainchain, Oxygen.
The attachment is a simple patch for src/tools/gmx_rmsf.c (v 1.3,
GROMACS 3.3) that solves the problem.
Cheers,
marco
-==_///_/-=-_/-=-_-==_//-//--/-
Marco Pasi, PhD Student
Department of Biotechnology and Biosciences
University of Milan-Bicocca
Piazza della Scienza, 2
20126 Milan - Italy
Phone: +39.02.64483475
E-mail: [EMAIL PROTECTED]
-=_///-=--_//=---=_/---///-==///--
*** gmx_rmsf.c 2004-02-02 13:33:28.0 +0100
--- gmx_rmsf-new.c 2007-04-19 22:08:36.0 +0200
*** int gmx_rmsf(int argc,char *argv[])
*** 352,365
}
sfree(U);
}
if (bRes) {
average_residues(rmsf,isize,index,w_rls,top.atoms);
label = Residue;
} else
label = Atom;
-
- for(i=0; iisize; i++)
- rmsf[i] = U[i][XX*DIM + XX] + U[i][YY*DIM + YY] + U[i][ZZ*DIM + ZZ];
if (dirfn) {
fprintf(stdout,\n);
--- 352,365
}
sfree(U);
}
+ for(i=0; iisize; i++)
+ rmsf[i] = U[i][XX*DIM + XX] + U[i][YY*DIM + YY] + U[i][ZZ*DIM + ZZ];
+
if (bRes) {
average_residues(rmsf,isize,index,w_rls,top.atoms);
label = Residue;
} else
label = Atom;
if (dirfn) {
fprintf(stdout,\n);
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
